Re:

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Fri Apr 08 2005 - 13:50:34 CDT

  I have written a simple fortran program to do that, but to convert
the charmm names as they are in the tinker package to the ones used in
namd. I don't know if the ones used by modeller are the same as the
ones used by tinker, but you can try it. Here I send it attached.
Compile this simple program and run it with

atomnames < test.pdb > newpdb.pdb

Leandro.

On Apr 8, 2005 2:31 PM, Michael Grabe <mgrabe_at_itsa.ucsf.edu> wrote:
> Hello Michel,
>
> So I am very particular about the placement of my
> initial hydrogens. This is why I use Modeller with the
> hydrogens turned on. I want to preserve the exact
> positions of all of the hydrogens when creating
> my initial PDB/PSF file using psfgen.
>
> Thanks,
> Michael
>
>
> On Apr 8, 2005, at 10:27 AM, Michel Espinoza-Fonseca wrote:
>
> > Hi Michael,
> >
> > I guess what you have to do is very easy. First of all, remove all
> > hydrogens from your protein using Swiss PDB viewer, for example. Then
> > save your pdb file WITHOUT hydrogens. After that, use the pdb file
> > without hydrogens to create your pdb and psf files, using psfgen
> > (psfgen will add the hydrogens automatically).
> >
> > If you have further questions, make me know…
> >
> > I hope it helps,
> >
> > Peace,
> >
> > Michel
> >
> >
> >
> >
> > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> > Behalf Of Michael Grabe
> > Sent: Friday, April 08, 2005 12:05 PM
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l:
> >
> >
> >
> > hello all,
> >
> >
> >
> > i use modeller to produce homology models with hydrogen atoms,
> >
> > and it seems that the naming convention for the hydrogens
> >
> > is different from the naming convention used inthe CHARMM files
> >
> > I use to create the topology files. I use psfgen for this step.
> >
> > I have tried to use the alias command for some of these but that
> >
> > is a lot of hydrogens.
> >
> >
> >
> > has some one compiled all of the correct aliases for the conversion
> >
> > between these two formats?
> >
> >
> >
> > thanks
> >
> > michael
> >
> >
> > -----------------------------------------------------------------------
> > ---------------------------
> >
> > Michael Grabe, Ph.D.
> >
> > HHMI/UCSF
> >
> > Genetics Development & Behavioral Science Building
> >
> > 1550 4th Street, GD 481
> >
> > San Francisco, CA 94143-0725
> >
> > tel: ++ 415.476.0421
> >
> > http://itsa.ucsf.edu/~mgrabe
> >
> >
> >
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> HHMI/UCSF
> Genetics Development & Behavioral Science Building
> 1550 4th Street, GD 481
> San Francisco, CA 94143-0725
> tel: ++ 415.476.0421
> http://itsa.ucsf.edu/~mgrabe
>
>


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